Charged polysaccharides as model polyelectrolytes : computational studies of transport and conformational properties : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Physics at Massey University, Palmerston North, New Zealand
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2018
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Massey University
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Abstract
Homogalacturonans (HGs) are polysaccharide co-polymers of galacturonic acid and
its methylesterified counterpart, that play a crucial role in the mechanobiology of the
cell walls of all land plants. When extracted, in solution, at pH values above the
pKa, the carboxyl groups carried by the unmethylesterified residues endow the polymer
chains with charge, making these systems interesting polyelectrolytes. The interand
intra-molecular distributions of the non-charged methylesterified residues and their
charged methylesterified counterparts are vital behaviour-determining characteristics
of a sample's structure. Previous work has led to the development of techniques for the
control of the amount and distribution of charges, and with these tools and samples
available in dfiferent degrees of polymerisation, including small oligomers, the system
offers a
flexible test-bed for studying the behaviour of biological polyelectrolytes.
This thesis is rooted in exploring the use of computational approaches, in particular
molecular dynamics, to calculate the conformation of such polyelectrolytes in solution
and to describe their transport properties in electric fields. The results of simulations
are, in all cases, compared with the results of experimental work in order to ground
the simulations.
First, in chapter 2, these simulations are applied to calculate the free solution electrophoretic
mobilities of galacturonides, charged oligosaccharides derived from digests
of partially methylesterified HGs. The simulations are compared with experiment
and were found to correctly predict the loss of resolution of electrophoretic mobilities
for fully-charged species above a critical degree of polymerisation (DP), and the
ionic strength dependence of the electrophoretic mobilities of different partially charged
oligosaccharides.
Next, in chapter 3, molecular dynamics (MD) simulations are used to calculate the electrophoretic
mobilities of HGs that have different amounts and distributions of charges
placed along the backbone. The simulations are shown to capture experimental results well even for samples that possess high charge densities. In addition they illuminate
the role that local counterion condensation can play in the determination of the electrophoretic
mobility of heterogeneous blocky polyelectrolytes that cannot be adequately
described by a single chain-averaged charge spacing.
Finally, in chapter 4, the last part of the research focusses on the configurations of
these polyelelectrolyes in dilute solution, and on how the interactions between several
chains can lead to the spatially heterogenous nature of polyelectrolyte solutions. Such
questions are of long standing interest in the polyelectrolyte field and the results are
compared with results from Small Angle X-Ray Scattering(SAXS).
Overall the work demonstrates how state of the art MD approaches can provide insights
into experimental results obtained from fundamentally interesting and biologically
relevent polyelectrolytes.
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Keywords
Polysaccharides, Polyelectrolytes, Biophysics, Computer simulation, Molecular dynamics